Nishigandha Phalke (Zhiping Weng)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 71

Top Venues

Science (New York, N.Y.)

Nucleic acids research

Proteins

Nature genetics

University of Massachusetts Medical School

Boston University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Massachusetts Medical School Jan 05 2008

United States

Director/Professor :: Program in Bioinformatics and Integrative Biology

Education History

Boston University

United States

PHD :: Biomedical Engineering

Publications

Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F Przytycki, Daniel D Vo, Arjun Bhattacharya, Nana Matoba, Miao Tang, Chuan Jiao, Minsoo Kim, Ellen Tsai, Celine Hoh, Nil Aygün, Rebecca L Walker, Christos Chatzinakos, Declan Clarke, Henry E Pratt, null null, Mette A Peters, Mark B Gerstein, Nikolaos P Daskalakis, Nishigandha Phalke, Andrew E Jaffe, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, Nicholas J Bray, Nenad Sestan, Daniel H Geschwind, Kathryn Roeder, Alexander Gusev, Bogdan Pasaniuc, Jason L Stein, Michael I Love, Katherine S Pollard, Yanling Liu, Michael J Gandal, null null
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science (New York, N.Y.) 384 (6698) (2024)
Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F Przytycki, Daniel D Vo, Arjun Bhattacharya, Nana Matoba, Miao Tang, Chuan Jiao, Minsoo Kim, Ellen Tsai, Celine Hoh, Nil Aygün, Rebecca L Walker, Christos Chatzinakos, Declan Clarke, Henry E Pratt, null null, Mette A Peters, Mark B Gerstein, Nikolaos P Daskalakis, Nishigandha Phalke, Andrew E Jaffe, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, Nicholas J Bray, Nenad Sestan, Daniel H Geschwind, Kathryn Roeder, Alexander Gusev, Bogdan Pasaniuc, Jason L Stein, Michael I Love, Katherine S Pollard, Yanling Liu, Michael J Gandal, null null
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F Przytycki, Daniel D Vo, Arjun Bhattacharya, Nana Matoba, Miao Tang, Chuan Jiao, Minsoo Kim, Ellen Tsai, Celine Hoh, Nil Aygün, Rebecca L Walker, Christos Chatzinakos, Declan Clarke, Henry E Pratt, null null, Mette A Peters, Mark B Gerstein, Nikolaos P Daskalakis, Nishigandha Phalke, Andrew E Jaffe, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, Nicholas J Bray, Nenad Sestan, Daniel H Geschwind, Kathryn Roeder, Alexander Gusev, Bogdan Pasaniuc, Jason L Stein, Michael I Love, Katherine S Pollard, Yanling Liu, Michael J Gandal, null null
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science (New York, N.Y.) 384 (6698) (2024)
Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F Przytycki, Daniel D Vo, Arjun Bhattacharya, Nana Matoba, Miao Tang, Chuan Jiao, Minsoo Kim, Ellen Tsai, Celine Hoh, Nil Aygün, Rebecca L Walker, Christos Chatzinakos, Declan Clarke, Henry E Pratt, null null, Mette A Peters, Mark B Gerstein, Nikolaos P Daskalakis, Nishigandha Phalke, Andrew E Jaffe, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, Nicholas J Bray, Nenad Sestan, Daniel H Geschwind, Kathryn Roeder, Alexander Gusev, Bogdan Pasaniuc, Jason L Stein, Michael I Love, Katherine S Pollard, Yanling Liu, Michael J Gandal, null null
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science (New York, N.Y.) 384 (6698) (2024)
Henry E Pratt, Gregory Andrews, Nicole Shedd, Nishigandha Phalke, Tongxin Li, Anusri Pampari, Matthew Jensen, Cindy Wen, PsychENCODE Consortium, Michael J Gandal, Daniel H Geschwind, Mark B Gerstein, Jill E Moore, Anshul Kundaje, Andres Colubri, Nishigandha Phalke
Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Science advances 10 (21) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Henry E Pratt, Gregory Andrews, Nicole Shedd, Nishigandha Phalke, Tongxin Li, Anusri Pampari, Matthew Jensen, Cindy Wen, PsychENCODE Consortium, Michael J Gandal, Daniel H Geschwind, Mark B Gerstein, Jill E Moore, Anshul Kundaje, Andres Colubri, Nishigandha Phalke
Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Science advances 10 (21) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Jichuan Cao, Tianxiong Yu, Bo Xu, Zhongren Hu, Xiao-Ou Zhang, William E Theurkauf, Nishigandha Phalke
Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. Nucleic acids research (2023)
Andreas R Gschwind, Kristy S Mualim, Alireza Karbalayghareh, Maya U Sheth, Kushal K Dey, Evelyn Jagoda, Ramil N Nurtdinov, Wang Xi, Anthony S Tan, Hank Jones, X Rosa Ma, David Yao, Joseph Nasser, Žiga Avsec, Benjamin T James, Muhammad Saad Shamim, Neva C Durand, Suhas S P Rao, Ragini Mahajan, Benjamin R Doughty, Kalina Andreeva, Jacob C Ulirsch, Kaili Fan, Elizabeth M Perez, Tri C Nguyen, David R Kelley, Hilary K Finucane, Jill E Moore, Nishigandha Phalke, Manolis Kellis, Michael C Bassik, Alkes L Price, Michael A Beer, Roderic Guigo, John A Stamatoyannopoulos, Erez Lieberman Aiden, William J Greenleaf, Christina S Leslie, Lars M Steinmetz, Anshul Kundaje, Jesse M Engreitz
An encyclopedia of enhancer-gene regulatory interactions in the human genome. bioRxiv : the preprint server for biology (2023)
Matthew J Christmas, Irene M Kaplow, Diane P Genereux, Michael X Dong, Graham M Hughes, Xue Li, Patrick F Sullivan, Allyson G Hindle, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Ana M Breit, Mark E Diekhans, Cornelia Fanter, Nicole M Foley, Daniel B Goodman, Linda Goodman, Kathleen C Keough, Bogdan M Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L Lind, Jennifer R S Meadows, Lucas R Moreira, Ruby W Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna R Grimshaw, Jeremy Johnson, Sergey V Kozyrev, Alyssa J Lawler, Voichita D Marinescu, Kathleen M Morrill, Austin B Osmanski, Nicole S Paulat, BaDoi N Phan, Steven K Reilly, Daniel E Schäffer, Cynthia C Steiner, Megan Ann Supple, Aryn P Wilder, Morgan E Wirthlin, James R Xue, null null, Bruce W Birren, Steven Gazal, Robert M Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K Meyer, Martin T Nweeia, Pardis C Sabeti, Joshua D Kapp, Arian F A Smit, Mark S Springer, Emma C Teeling, Nishigandha Phalke, Michael Hiller, Danielle L Levesque, Harris A Lewin, William J Murphy, Arcadi Navarro, Benedict Paten, Katherine S Pollard, David A Ray, Irina Ruf, Oliver A Ryder, Andreas R Pfenning, Kerstin Lindblad-Toh, Elinor K Karlsson, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.) 380 (6643) (2023)
Patrick F Sullivan, Jennifer R S Meadows, Steven Gazal, BaDoi N Phan, Xue Li, Diane P Genereux, Michael X Dong, Matteo Bianchi, Gregory Andrews, Sharadha Sakthikumar, Jessika Nordin, Ananya Roy, Matthew J Christmas, Voichita D Marinescu, Chao Wang, Ola Wallerman, James R Xue, Shuyang Yao, Quan Sun, Jin P Szatkiewicz, Jia Wen, Laura M Huckins, Alyssa J Lawler, Kathleen C Keough, Zhili Zheng, Jian Zeng, Naomi R Wray, Yun Li, Jessica S Johnson, Jiawen Chen, null null, Benedict Paten, Steven K Reilly, Graham M Hughes, Nishigandha Phalke, Katherine S Pollard, Andreas R Pfenning, Karin Forsberg-Nilsson, Elinor K Karlsson, Kerstin Lindblad-Toh, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.) 380 (6643) (2023)
Matthew J Christmas, Irene M Kaplow, Diane P Genereux, Michael X Dong, Graham M Hughes, Xue Li, Patrick F Sullivan, Allyson G Hindle, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Ana M Breit, Mark E Diekhans, Cornelia Fanter, Nicole M Foley, Daniel B Goodman, Linda Goodman, Kathleen C Keough, Bogdan M Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L Lind, Jennifer R S Meadows, Lucas R Moreira, Ruby W Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna R Grimshaw, Jeremy Johnson, Sergey V Kozyrev, Alyssa J Lawler, Voichita D Marinescu, Kathleen M Morrill, Austin B Osmanski, Nicole S Paulat, BaDoi N Phan, Steven K Reilly, Daniel E Schäffer, Cynthia C Steiner, Megan Ann Supple, Aryn P Wilder, Morgan E Wirthlin, James R Xue, null null, Bruce W Birren, Steven Gazal, Robert M Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K Meyer, Martin T Nweeia, Pardis C Sabeti, Joshua D Kapp, Arian F A Smit, Mark S Springer, Emma C Teeling, Nishigandha Phalke, Michael Hiller, Danielle L Levesque, Harris A Lewin, William J Murphy, Arcadi Navarro, Benedict Paten, Katherine S Pollard, David A Ray, Irina Ruf, Oliver A Ryder, Andreas R Pfenning, Kerstin Lindblad-Toh, Elinor K Karlsson, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.) 380 (6643) (2023)
Gregory Andrews, Kaili Fan, Henry E Pratt, Nishigandha Phalke, null null, Elinor K Karlsson, Kerstin Lindblad-Toh, Steven Gazal, Jill E Moore, Nishigandha Phalke
Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (New York, N.Y.) 380 (6643) (2023)
Gregory Andrews, Kaili Fan, Henry E Pratt, Nishigandha Phalke, null null, Elinor K Karlsson, Kerstin Lindblad-Toh, Steven Gazal, Jill E Moore, Nishigandha Phalke
Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (New York, N.Y.) 380 (6643) (2023)
Matthew J Christmas, Irene M Kaplow, Diane P Genereux, Michael X Dong, Graham M Hughes, Xue Li, Patrick F Sullivan, Allyson G Hindle, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Ana M Breit, Mark E Diekhans, Cornelia Fanter, Nicole M Foley, Daniel B Goodman, Linda Goodman, Kathleen C Keough, Bogdan M Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L Lind, Jennifer R S Meadows, Lucas R Moreira, Ruby W Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna R Grimshaw, Jeremy Johnson, Sergey V Kozyrev, Alyssa J Lawler, Voichita D Marinescu, Kathleen M Morrill, Austin B Osmanski, Nicole S Paulat, BaDoi N Phan, Steven K Reilly, Daniel E Schäffer, Cynthia C Steiner, Megan Ann Supple, Aryn P Wilder, Morgan E Wirthlin, James R Xue, null null, Bruce W Birren, Steven Gazal, Robert M Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K Meyer, Martin T Nweeia, Pardis C Sabeti, Joshua D Kapp, Arian F A Smit, Mark S Springer, Emma C Teeling, Nishigandha Phalke, Michael Hiller, Danielle L Levesque, Harris A Lewin, William J Murphy, Arcadi Navarro, Benedict Paten, Katherine S Pollard, David A Ray, Irina Ruf, Oliver A Ryder, Andreas R Pfenning, Kerstin Lindblad-Toh, Elinor K Karlsson
Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.) 380 (6643) (2023)
Jichuan Cao, Tianxiong Yu, Bo Xu, Zhongren Hu, Xiao-Ou Zhang, William E Theurkauf, Nishigandha Phalke
Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. Nucleic acids research 51 (5) (2023)
Gregory Andrews, Kaili Fan, Henry E Pratt, Nishigandha Phalke, null null, Elinor K Karlsson, Kerstin Lindblad-Toh, Steven Gazal, Jill E Moore, Nishigandha Phalke, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (New York, N.Y.) 380 (6643) (2023)
Gregory Andrews, Kaili Fan, Henry E Pratt, Nishigandha Phalke, null null, Elinor K Karlsson, Kerstin Lindblad-Toh, Steven Gazal, Jill E Moore, Nishigandha Phalke, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (New York, N.Y.) 380 (6643) (2023)
Patrick F Sullivan, Jennifer R S Meadows, Steven Gazal, BaDoi N Phan, Xue Li, Diane P Genereux, Michael X Dong, Matteo Bianchi, Gregory Andrews, Sharadha Sakthikumar, Jessika Nordin, Ananya Roy, Matthew J Christmas, Voichita D Marinescu, Chao Wang, Ola Wallerman, James R Xue, Shuyang Yao, Quan Sun, Jin P Szatkiewicz, Jia Wen, Laura M Huckins, Alyssa J Lawler, Kathleen C Keough, Zhili Zheng, Jian Zeng, Naomi R Wray, Yun Li, Jessica S Johnson, Jiawen Chen, null null, Benedict Paten, Steven K Reilly, Graham M Hughes, Nishigandha Phalke, Katherine S Pollard, Andreas R Pfenning, Karin Forsberg-Nilsson, Elinor K Karlsson, Kerstin Lindblad-Toh, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.) 380 (6643) (2023)
Gregory Andrews, Kaili Fan, Henry E Pratt, Nishigandha Phalke, null null, Elinor K Karlsson, Kerstin Lindblad-Toh, Steven Gazal, Jill E Moore, Nishigandha Phalke, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (New York, N.Y.) 380 (6643) (2023)
Gregory Andrews, Kaili Fan, Henry E Pratt, Nishigandha Phalke, null null, Elinor K Karlsson, Kerstin Lindblad-Toh, Steven Gazal, Jill E Moore, Nishigandha Phalke, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (New York, N.Y.) 380 (6643) (2023)
Gregory Andrews, Kaili Fan, Henry E Pratt, Nishigandha Phalke, null null, Elinor K Karlsson, Kerstin Lindblad-Toh, Steven Gazal, Jill E Moore, Nishigandha Phalke
Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (New York, N.Y.) 380 (6643) (2023)
Patrick F Sullivan, Jennifer R S Meadows, Steven Gazal, BaDoi N Phan, Xue Li, Diane P Genereux, Michael X Dong, Matteo Bianchi, Gregory Andrews, Sharadha Sakthikumar, Jessika Nordin, Ananya Roy, Matthew J Christmas, Voichita D Marinescu, Chao Wang, Ola Wallerman, James R Xue, Shuyang Yao, Quan Sun, Jin P Szatkiewicz, Jia Wen, Laura M Huckins, Alyssa J Lawler, Kathleen C Keough, Zhili Zheng, Jian Zeng, Naomi R Wray, Yun Li, Jessica S Johnson, Jiawen Chen, null null, Benedict Paten, Steven K Reilly, Graham M Hughes, Nishigandha Phalke, Katherine S Pollard, Andreas R Pfenning, Karin Forsberg-Nilsson, Elinor K Karlsson, Kerstin Lindblad-Toh, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.) 380 (6643) (2023)
Patrick F Sullivan, Jennifer R S Meadows, Steven Gazal, BaDoi N Phan, Xue Li, Diane P Genereux, Michael X Dong, Matteo Bianchi, Gregory Andrews, Sharadha Sakthikumar, Jessika Nordin, Ananya Roy, Matthew J Christmas, Voichita D Marinescu, Chao Wang, Ola Wallerman, James R Xue, Shuyang Yao, Quan Sun, Jin P Szatkiewicz, Jia Wen, Laura M Huckins, Alyssa J Lawler, Kathleen C Keough, Zhili Zheng, Jian Zeng, Naomi R Wray, Yun Li, Jessica S Johnson, Jiawen Chen, null null, Benedict Paten, Steven K Reilly, Graham M Hughes, Nishigandha Phalke, Katherine S Pollard, Andreas R Pfenning, Karin Forsberg-Nilsson, Elinor K Karlsson, Kerstin Lindblad-Toh, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.) 380 (6643) (2023)
Kaili Fan, Edith L Pfister, Nishigandha Phalke
Toward a comprehensive catalog of regulatory elements. Human genetics (2023)
Matthew J Christmas, Irene M Kaplow, Diane P Genereux, Michael X Dong, Graham M Hughes, Xue Li, Patrick F Sullivan, Allyson G Hindle, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Ana M Breit, Mark E Diekhans, Cornelia Fanter, Nicole M Foley, Daniel B Goodman, Linda Goodman, Kathleen C Keough, Bogdan M Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L Lind, Jennifer R S Meadows, Lucas R Moreira, Ruby W Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna R Grimshaw, Jeremy Johnson, Sergey V Kozyrev, Alyssa J Lawler, Voichita D Marinescu, Kathleen M Morrill, Austin B Osmanski, Nicole S Paulat, BaDoi N Phan, Steven K Reilly, Daniel E Schäffer, Cynthia C Steiner, Megan Ann Supple, Aryn P Wilder, Morgan E Wirthlin, James R Xue, null null, Bruce W Birren, Steven Gazal, Robert M Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K Meyer, Martin T Nweeia, Pardis C Sabeti, Joshua D Kapp, Arian F A Smit, Mark S Springer, Emma C Teeling, Nishigandha Phalke, Michael Hiller, Danielle L Levesque, Harris A Lewin, William J Murphy, Arcadi Navarro, Benedict Paten, Katherine S Pollard, David A Ray, Irina Ruf, Oliver A Ryder, Andreas R Pfenning, Kerstin Lindblad-Toh, Elinor K Karlsson, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.) 380 (6643) (2023)
Matthew J Christmas, Irene M Kaplow, Diane P Genereux, Michael X Dong, Graham M Hughes, Xue Li, Patrick F Sullivan, Allyson G Hindle, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Ana M Breit, Mark E Diekhans, Cornelia Fanter, Nicole M Foley, Daniel B Goodman, Linda Goodman, Kathleen C Keough, Bogdan M Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L Lind, Jennifer R S Meadows, Lucas R Moreira, Ruby W Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna R Grimshaw, Jeremy Johnson, Sergey V Kozyrev, Alyssa J Lawler, Voichita D Marinescu, Kathleen M Morrill, Austin B Osmanski, Nicole S Paulat, BaDoi N Phan, Steven K Reilly, Daniel E Schäffer, Cynthia C Steiner, Megan Ann Supple, Aryn P Wilder, Morgan E Wirthlin, James R Xue, null null, Bruce W Birren, Steven Gazal, Robert M Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K Meyer, Martin T Nweeia, Pardis C Sabeti, Joshua D Kapp, Arian F A Smit, Mark S Springer, Emma C Teeling, Nishigandha Phalke, Michael Hiller, Danielle L Levesque, Harris A Lewin, William J Murphy, Arcadi Navarro, Benedict Paten, Katherine S Pollard, David A Ray, Irina Ruf, Oliver A Ryder, Andreas R Pfenning, Kerstin Lindblad-Toh, Elinor K Karlsson, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.) 380 (6643) (2023)
Jichuan Cao, Tianxiong Yu, Bo Xu, Zhongren Hu, Xiao-Ou Zhang, William E Theurkauf, Nishigandha Phalke
Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. Nucleic acids research 51 (5) (2023)
Patrick F Sullivan, Jennifer R S Meadows, Steven Gazal, BaDoi N Phan, Xue Li, Diane P Genereux, Michael X Dong, Matteo Bianchi, Gregory Andrews, Sharadha Sakthikumar, Jessika Nordin, Ananya Roy, Matthew J Christmas, Voichita D Marinescu, Chao Wang, Ola Wallerman, James R Xue, Shuyang Yao, Quan Sun, Jin P Szatkiewicz, Jia Wen, Laura M Huckins, Alyssa J Lawler, Kathleen C Keough, Zhili Zheng, Jian Zeng, Naomi R Wray, Yun Li, Jessica S Johnson, Jiawen Chen, null null, Benedict Paten, Steven K Reilly, Graham M Hughes, Nishigandha Phalke, Katherine S Pollard, Andreas R Pfenning, Karin Forsberg-Nilsson, Elinor K Karlsson, Kerstin Lindblad-Toh
Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.) 380 (6643) (2023)
Patrick F Sullivan, Jennifer R S Meadows, Steven Gazal, BaDoi N Phan, Xue Li, Diane P Genereux, Michael X Dong, Matteo Bianchi, Gregory Andrews, Sharadha Sakthikumar, Jessika Nordin, Ananya Roy, Matthew J Christmas, Voichita D Marinescu, Chao Wang, Ola Wallerman, James R Xue, Shuyang Yao, Quan Sun, Jin P Szatkiewicz, Jia Wen, Laura M Huckins, Alyssa J Lawler, Kathleen C Keough, Zhili Zheng, Jian Zeng, Naomi R Wray, Yun Li, Jessica S Johnson, Jiawen Chen, null null, Benedict Paten, Steven K Reilly, Graham M Hughes, Nishigandha Phalke, Katherine S Pollard, Andreas R Pfenning, Karin Forsberg-Nilsson, Elinor K Karlsson, Kerstin Lindblad-Toh
Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.) 380 (6643) (2023)
Fairlie Reese, Brian A Williams, Gabriela Balderrama-Gutierrez, Dana Wyman, Muhammed Hasan Çelik, Elisabeth Rebboah, Narges Rezaie, Diane Trout, Milad Razavi-Mohseni, Yunzhe Jiang, Beatrice Borsari, Samuel J Morabito, Heidi Yahan Liang, Cassandra J McGill, Sorena Rahmanian, Jasmine Sakr, Shan Jiang, Weihua Zeng, Klebea Carvalho, Annika K Weimer, Louise A Dionne, Ariel McShane, Karan Bedi, Shaimae I Elhajjajy, Sean Upchurch, Jennifer Jou, Ingrid Youngworth, Aditi K Narayanan, Paul Sud, Otto Jolanki, Benjamin C Hitz, Meenakshi S Kagda, Michael Paul Snyder, Benjamin C Hitz, Jill E Moore, Nishigandha Phalke, David A Bennett, Laura G Reinholdt, Mats Ljungman, Michael A Beer, Mark B Gerstein, Lior Pachter, Roderic Guigo, Barbara J Wold, Ali Mortazavi
The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv : the preprint server for biology (2023)
Gregory Andrews, Kaili Fan, Henry E Pratt, Nishigandha Phalke, null null, Elinor K Karlsson, Kerstin Lindblad-Toh, Steven Gazal, Jill E Moore, Nishigandha Phalke, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (New York, N.Y.) 380 (6643) (2023)
Matthew J Christmas, Irene M Kaplow, Diane P Genereux, Michael X Dong, Graham M Hughes, Xue Li, Patrick F Sullivan, Allyson G Hindle, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Ana M Breit, Mark E Diekhans, Cornelia Fanter, Nicole M Foley, Daniel B Goodman, Linda Goodman, Kathleen C Keough, Bogdan M Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L Lind, Jennifer R S Meadows, Lucas R Moreira, Ruby W Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna R Grimshaw, Jeremy Johnson, Sergey V Kozyrev, Alyssa J Lawler, Voichita D Marinescu, Kathleen M Morrill, Austin B Osmanski, Nicole S Paulat, BaDoi N Phan, Steven K Reilly, Daniel E Schäffer, Cynthia C Steiner, Megan Ann Supple, Aryn P Wilder, Morgan E Wirthlin, James R Xue, null null, Bruce W Birren, Steven Gazal, Robert M Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K Meyer, Martin T Nweeia, Pardis C Sabeti, Joshua D Kapp, Arian F A Smit, Mark S Springer, Emma C Teeling, Nishigandha Phalke, Michael Hiller, Danielle L Levesque, Harris A Lewin, William J Murphy, Arcadi Navarro, Benedict Paten, Katherine S Pollard, David A Ray, Irina Ruf, Oliver A Ryder, Andreas R Pfenning, Kerstin Lindblad-Toh, Elinor K Karlsson, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.) 380 (6643) (2023)
Matthew J Christmas, Irene M Kaplow, Diane P Genereux, Michael X Dong, Graham M Hughes, Xue Li, Patrick F Sullivan, Allyson G Hindle, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Ana M Breit, Mark E Diekhans, Cornelia Fanter, Nicole M Foley, Daniel B Goodman, Linda Goodman, Kathleen C Keough, Bogdan M Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L Lind, Jennifer R S Meadows, Lucas R Moreira, Ruby W Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna R Grimshaw, Jeremy Johnson, Sergey V Kozyrev, Alyssa J Lawler, Voichita D Marinescu, Kathleen M Morrill, Austin B Osmanski, Nicole S Paulat, BaDoi N Phan, Steven K Reilly, Daniel E Schäffer, Cynthia C Steiner, Megan Ann Supple, Aryn P Wilder, Morgan E Wirthlin, James R Xue, null null, Bruce W Birren, Steven Gazal, Robert M Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K Meyer, Martin T Nweeia, Pardis C Sabeti, Joshua D Kapp, Arian F A Smit, Mark S Springer, Emma C Teeling, Nishigandha Phalke, Michael Hiller, Danielle L Levesque, Harris A Lewin, William J Murphy, Arcadi Navarro, Benedict Paten, Katherine S Pollard, David A Ray, Irina Ruf, Oliver A Ryder, Andreas R Pfenning, Kerstin Lindblad-Toh, Elinor K Karlsson
Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.) 380 (6643) (2023)
Patrick F Sullivan, Jennifer R S Meadows, Steven Gazal, BaDoi N Phan, Xue Li, Diane P Genereux, Michael X Dong, Matteo Bianchi, Gregory Andrews, Sharadha Sakthikumar, Jessika Nordin, Ananya Roy, Matthew J Christmas, Voichita D Marinescu, Chao Wang, Ola Wallerman, James R Xue, Shuyang Yao, Quan Sun, Jin P Szatkiewicz, Jia Wen, Laura M Huckins, Alyssa J Lawler, Kathleen C Keough, Zhili Zheng, Jian Zeng, Naomi R Wray, Yun Li, Jessica S Johnson, Jiawen Chen, null null, Benedict Paten, Steven K Reilly, Graham M Hughes, Nishigandha Phalke, Katherine S Pollard, Andreas R Pfenning, Karin Forsberg-Nilsson, Elinor K Karlsson, Kerstin Lindblad-Toh, Gregory Andrews, Joel C Armstrong, Matteo Bianchi, Bruce W Birren, Kevin R Bredemeyer, Ana M Breit, Matthew J Christmas, Hiram Clawson, Joana Damas, Federica Di Palma, Mark Diekhans, Michael X Dong, Eduardo Eizirik, Kaili Fan, Cornelia Fanter, Nicole M Foley, Karin Forsberg-Nilsson, Carlos J Garcia, John Gatesy, Steven Gazal, Diane P Genereux, Linda Goodman, Jenna Grimshaw, Michaela K Halsey, Andrew J Harris, Glenn Hickey, Michael Hiller, Allyson G Hindle, Robert M Hubley, Graham M Hughes, Jeremy Johnson, David Juan, Irene M Kaplow, Elinor K Karlsson, Kathleen C Keough, Bogdan Kirilenko, Klaus-Peter Koepfli, Jennifer M Korstian, Amanda Kowalczyk, Sergey V Kozyrev, Alyssa J Lawler, Colleen Lawless, Thomas Lehmann, Danielle L Levesque, Harris A Lewin, Xue Li, Abigail Lind, Kerstin Lindblad-Toh, Ava Mackay-Smith, Voichita D Marinescu, Tomas Marques-Bonet, Victor C Mason, Jennifer R S Meadows, Wynn K Meyer, Jill E Moore, Lucas R Moreira, Diana D Moreno-Santillan, Kathleen M Morrill, Gerard Muntané, William J Murphy, Arcadi Navarro, Martin Nweeia, Sylvia Ortmann, Austin Osmanski, Benedict Paten, Nicole S Paulat, Andreas R Pfenning, BaDoi N Phan, Katherine S Pollard, Henry E Pratt, David A Ray, Steven K Reilly, Jeb R Rosen, Irina Ruf, Louise Ryan, Oliver A Ryder, Pardis C Sabeti, Daniel E Schäffer, Aitor Serres, Beth Shapiro, Arian F A Smit, Mark Springer, Chaitanya Srinivasan, Cynthia Steiner, Jessica M Storer, Kevin A M Sullivan, Patrick F Sullivan, Elisabeth Sundström, Megan A Supple, Ross Swofford, Joy-El Talbot, Emma Teeling, Jason Turner-Maier, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Chao Wang, Juehan Wang, Zhiping Weng, Aryn P Wilder, Morgan E Wirthlin, James R Xue, Xiaomeng Zhang
Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.) 380 (6643) (2023)
Jichuan Cao, Tianxiong Yu, Bo Xu, Zhongren Hu, Xiao-Ou Zhang, William E Theurkauf, Nishigandha Phalke
Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. Nucleic acids research (2023)
Zixiu Li, Peng Zhou, Euijin Kwon, Katherine A Fitzgerald, Nishigandha Phalke, Chan Zhou
Flnc: Machine Learning Improves the Identification of Novel Long Noncoding RNAs from Stand-Alone RNA-Seq Data. Non-coding RNA 8 (5) (2022)
Tianxiong Yu, Adriano Biasini, Katharine Cecchini, Martin Saflund, Haiwei Mou, Amena Arif, Atiyeh Eghbali, Dirk G de Rooij, Nishigandha Phalke, Phillip D Zamore, Deniz M Özata
A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammals. RNA (New York, N.Y.) (2022)
Wenjun Chen, Jordan S Brown, Tao He, Wei-Sheng Wu, Shikui Tu, Nishigandha Phalke, Donglei Zhang, Heng-Chi Lee
GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance. Nature communications 13 (1) (2022)
Kathleen M Morrill, Jessica P Hekman, Xue Li, Jesse McClure, Brittney Logan, Linda Goodman, Mingshi Gao, Yinan Dong, Marjie Alonso, Elena Carmichael, Noah James Snyder-Mackler, Jacob Alonso, Hyun Ji Noh, Jeremy Johnson, Michele Koltookian, Charlie Lieu, Kate Megquier, Ross Swofford, Jason Turner-Maier, Michelle E White, Nishigandha Phalke, Andres Colubri, Diane P Genereux, Kathryn A Lord, Elinor K Karlsson
Ancestry-inclusive dog genomics challenges popular breed stereotypes. Science (New York, N.Y.) 376 (6592) (2022)
Jinrui Xu, Henry E Pratt, Jill E Moore, Mark B Gerstein, Nishigandha Phalke
Building integrative functional maps of gene regulation. Human molecular genetics 31 (R1) (2022)
I-Hao Wang, Evan Murray, Greg Andrews, Hao-Ching Jiang, Sung Jin Park, Elisa Donnard, Violeta Durán-Laforet, Daniel M Bear, Travis E Faust, Manuel Garber, Christina E Baer, Dorothy P Schafer, Nishigandha Phalke, Fei Chen, Evan Z Macosko, Paul L Greer
Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing. Nature neuroscience 25 (4) (2022)
Arjan van der Velde, Kaili Fan, Junko Tsuji, Jill E Moore, Michael J Purcaro, Henry E Pratt, Nishigandha Phalke
Annotation of chromatin states in 66 complete mouse epigenomes during development. Communications biology 4 (1) (2021)
Kaili Fan, Jill E Moore, Xiao-Ou Zhang, Nishigandha Phalke
Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes. Nucleic acids research 49 (10) (2021)
Henry E Pratt, Gregory R Andrews, Nishigandha Phalke, Michael J Purcaro, Arjan van der Velde, Jill E Moore, Zhiping Weng
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. Nucleic acids research (2021)
Tianxiong Yu, Xiao Huang, Shengqian Dou, Xiaolu Tang, Shiqi Luo, William E Theurkauf, Jian Lu, Nishigandha Phalke
A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies. Nucleic acids research 49 (8) (2021)
Lizhi He, Henry Pratt, Mingshi Gao, Fengxiang Wei, Nishigandha Phalke, Kevin Struhl
YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation. eLife 10 (2021)
Jill E Moore, Xiao-Ou Zhang, Shaimae I Elhajjajy, Kaili Fan, Henry E Pratt, Fairlie Reese, Ali Mortazavi, Nishigandha Phalke
Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types. Genome research 32 (2) (2021)
Houda Belaghzal, Tyler Borrman, Andrew D Stephens, Denis L Lafontaine, Sergey V Venev, Nishigandha Phalke, John F Marko, Job Dekker
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Nature genetics 53 (3) (2021)
Tianxiong Yu, Kaili Fan, Deniz M Özata, Gen Zhang, Yu Fu, William E Theurkauf, Phillip D Zamore, Nishigandha Phalke
Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes. Nature communications 12 (1) (2021)
Xihao Li, Zilin Li, Hufeng Zhou, Sheila M Gaynor, Yaowu Liu, Han Chen, Ryan Sun, Rounak Dey, Donna K Arnett, Stella Aslibekyan, Christie M Ballantyne, Lawrence F Bielak, John E Blangero, Eric Boerwinkle, Donald W Bowden, Jai G Broome, Matthew P Conomos, Adolfo Correa, L Adrienne Cupples, Joanne E Curran, Barry I Freedman, Xiuqing Guo, George Hindy, Marguerite R Irvin, Sharon L R Kardia, Sekar Kathiresan, Alyna T Khan, Charles L Kooperberg, Cathy C Laurie, X Shirley Liu, Michael C Mahaney, Ani W Manichaikul, Lisa Warsinger Martin, Rasika A Mathias, Stephen T McGarvey, Braxton D Mitchell, May E Montasser, Jill E Moore, Alanna C Morrison, Jeffrey R O'Connell, Nicholette D D Allred, Akhil Pampana, Juan M Peralta, Patricia A Peyser, Bruce M Psaty, Susan Redline, Kenneth M Rice, Stephen S Rich, Jennifer A Smith, Hemant K Tiwari, Michael Y Tsai, Ramachandran S Vasan, Fei Fei Wang, Daniel E Weeks, Nishigandha Phalke, James G Wilson, Lisa R Yanek, null null, null null, Benjamin M Neale, Shamil R Sunyaev, Gonçalo R Abecasis, Jerome I Rotter, Cristen J Willer, Gina M Peloso, Pradeep Natarajan, Xihong Lin
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nature genetics 52 (9) (2020)
Thom Vreven, Sweta Vangaveti, Tyler M Borrman, Jennifer C Gaines, Nishigandha Phalke
Performance of ZDOCK and IRAD in CAPRI rounds 39-45. Proteins 88 (8) (2020)
Pei-Hsuan Wu, Yu Fu, Katharine Cecchini, Deniz M Özata, Amena Arif, Tianxiong Yu, Cansu Colpan, Ildar V Gainetdinov, Nishigandha Phalke, Phillip D Zamore
The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility. Nature genetics 52 (7) (2020)
Alison P Casserly, Junko Tsuji, Rubing Zhao-Shea, Ciearra B Smith, Susanna Molas, Andrew R Tapper, Nishigandha Phalke, Paul D Gardner
Integrated miRNA-/mRNA-Seq of the Habenulo-Interpeduncular Circuit During Acute Nicotine Withdrawal. Scientific reports 10 (1) (2020)
Jill E Moore, Henry E Pratt, Michael J Purcaro, Nishigandha Phalke
A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods. Genome biology 21 (1) (2020)
null null, Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L Van Nostrand, Peter Freese, David U Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A Williams, Ali Mortazavi, Cheryl A Keller, Xiao-Ou Zhang, Shaimae I Elhajjajy, Jack Huey, Diane E Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B Chhetri, Jialing Zhang, Alec Victorsen, Kevin P White, Axel Visel, Gene W Yeo, Christopher B Burge, Eric Lécuyer, David M Gilbert, Job Dekker, John L Rinn, Eric M Mendenhall, Joseph R Ecker, Manolis Kellis, Robert J Klein, William S Noble, Anshul Kundaje, Roderic Guigó, Peggy J Farnham, J Michael Cherry, Richard M Myers, Bing Ren, Brenton R Graveley, Mark B Gerstein, Len A Pennacchio, Michael Paul Snyder, Bradley E Bernstein, Barbara Wold, Ross Cameron Hardison, Thomas R Gingeras, John A Stamatoyannopoulos, Nishigandha Phalke
Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583 (7818) (2020)
Prashanth Rajarajan, Tyler Borrman, Will Liao, Nadine Schrode, Erin Flaherty, Charlize Casiño, Samuel K Powell, Chittampalli Yashaswini, Elizabeth A LaMarca, Bibi Kassim, Behnam Javidfar, Sergio Espeso-Gil, Aiqun Li, Hyejung Won, Daniel H Geschwind, Seok-Man Ho, Matthew MacDonald, Gabriel E Hoffman, Panagiotis Roussos, Bin Zhang, Chang-Gyu Hahn, Nishigandha Phalke, Kristen J Brennand, Schahram Akbarian
Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk. Science (New York, N.Y.) 362 (6420) (2019)
Xiao-Ou Zhang, Thomas R Gingeras, Nishigandha Phalke
Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. Genome research 29 (9) (2019)
Marc F Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphael A G Chaleil, Tereza Gerguri, Paul A Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran-Ran Liu, Xi-Ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov, Adam Liwo, Silvia Crivelli, Guillaume Pagès, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng-You Huang, Mireia Rosell, Luis A Rodríguez-Lumbreras, Miguel Romero-Durana, Lucía Díaz-Bueno, Juan Fernández-Recio, Charles W Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subraman, Daisuke Kihara, Dima Kozakov, Sandor Vajda, Kathryn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain H Moal, David W Ritchie, Isaure Chauvot de Beauchene, Bernard Maigret, Marie-Dominique Devignes, Maria E Ruiz Echartea, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yue Cao, Yang Shen, Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok, Merav Braitbard, Lirane Bitton, Dina Scheidman-Duhovny, Justas Dapkunas, Kliment Olechnovič, Česlovas Venclovas, Petras J Kundrotas, Saveliy Belkin, Devlina Chakravarty, Varsha D Badal, Ilya A Vakser, Thom Vreven, Sweta Vangaveti, Tyler Borrman, Nishigandha Phalke, Johnathan D Guest, Ragul Gowthaman, Brian G Pierce, Xianjin Xu, Rui Duan, Liming Qiu, Jie Hou, Benjamin Ryan Merideth, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Panagiotis I Koukos, Jorge Roel-Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E Trellet, Adrien S J Melquiond, Li Xue, Brian Jiménez-García, Charlotte W van Noort, Rodrigo V Honorato, Alexandre M J J Bonvin, Shoshana J Wodak
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins 87 (12) (2019)
Deniz M Özata, Tianxiong Yu, Haiwei Mou, Ildar V Gainetdinov, Cansu Colpan, Katharine Cecchini, Yasin Kaymaz, Pei-Hsuan Wu, Kaili Fan, Alper Kucukural, Nishigandha Phalke, Phillip D Zamore
Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans. Nature ecology & evolution 4 (1) (2019)
Fedor E Gusev, Denis A Reshetov, Amanda C Mitchell, Tatiana V Andreeva, Aslihan Dincer, Anastasia P Grigorenko, Gennady Fedonin, Tobias Halene, Maria Aliseychik, Elena Filippova, Nishigandha Phalke, Schahram Akbarian, Evgeny I Rogaev
Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. Translational psychiatry 9 (1) (2019)
Xiao-Ou Zhang, Yu Fu, Haiwei Mou, Wen Xue, Nishigandha Phalke
The temporal landscape of recursive splicing during Pol II transcription elongation in human cells. PLoS genetics 14 (8) (2018)
Kiran Girdhar, Gabriel E Hoffman, Yan Jiang, Leanne Brown, Marija Kundakovic, Mads Engel Hauberg, Nancy J Francoeur, Ying-Chih Wang, Hardik Shah, David H Kavanagh, Elizabeth Zharovsky, Rivka Jacobov, Jennifer R Wiseman, Royce Park, Jessica S Johnson, Bibi S Kassim, Laura Sloofman, Eugenio Mattei, Nishigandha Phalke, Solveig K Sieberts, Mette A Peters, Brent T Harris, Barbara K Lipska, Pamela Sklar, Panagiotis Roussos, Schahram Akbarian
Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome. Nature neuroscience 21 (8) (2018)
Donglei Zhang, Shikui Tu, Michael W Stubna, Wei-Sheng Wu, Wei-Che Huang, Nishigandha Phalke, Heng-Chi Lee
The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes. Science (New York, N.Y.) 359 (6375) (2018)
Tyler Borrman, Jennifer Cimons, Michael Cosiano, Michael Purcaro, Brian G Pierce, Brian M Baker, Nishigandha Phalke
ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes. Proteins 85 (5) (2017)

Nishigandha Phalke.css-eqlu8i{font-size:small;padding-left:4px;} (Zhiping Weng)

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Nishigandha Phalke (Zhiping Weng)